PMC:7605337 / 11742-13001
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T39 | 105-112 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T40 | 284-291 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T41 | 790-797 | Body_part | denotes | alanine | http://purl.org/sig/ont/fma/fma82749 |
| T42 | 996-1000 | Body_part | denotes | hand | http://purl.org/sig/ont/fma/fma9712 |
| T43 | 1058-1064 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T2 | 996-1000 | Body_part | denotes | hand | http://purl.obolibrary.org/obo/UBERON_0002398 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T88 | 43-52 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T89 | 89-93 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T90 | 225-234 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T91 | 320-324 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T92 | 360-364 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T93 | 450-459 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T94 | 589-598 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T95 | 665-674 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T96 | 1087-1096 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T84 | 729-730 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T85 | 968-970 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T86 | 1219-1221 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T45 | 105-112 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T46 | 284-291 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T47 | 790-797 | Chemical | denotes | alanine | http://purl.obolibrary.org/obo/CHEBI_16449 |
| T48 | 968-970 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T60 | 0-42 | Sentence | denotes | Sequence Comparison and Mutant Preparation |
| T61 | 43-711 | Sentence | denotes | nCOV-2019 shares 76% sequence similarity with SARS-2002 spike protein, 73% sequence identity for RBD and 50% for the RBM.1 Bat coronavirus RaTG13 seems to be the closest relative of nCOV-2019 sharing about 93% sequence identity in the spike protein.6 The sequence alignment of SARS-2002 (accession number: AFR58742), SARS-civet (accession number: AY304486.1), Bat RaTG13 (accession number: MN996532.1), and nCOV-2019 (accession number: MN908947.1) is shown in Figure 2.6 To investigate the roles of critical mutations on the complex stability of nCOV-2019 with ACE2, mCSM-PPI2 webserver32 was used to find the residues in nCOV-2019 that are at the interface with ACE2. |
| T62 | 712-982 | Sentence | denotes | This method uses a graph-based signature framework and predicts the effect of alanine substitution at interface residues on the binding energy of the complex, and 21 different residues were identified to be in contact with ACE2 and were chosen for further MD simulation. |
| T63 | 983-1259 | Sentence | denotes | On the other hand, mutations are also observed in the RBD domain from full genome analysis of different nCOV-2019 variants collected from different countries compiled in the GISAID database.24 The mutations selected are listed in Table S1 along with their location in the RBD. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 333 | 278-283 | Gene | denotes | spike | Gene:43740568 |
| 334 | 604-608 | Gene | denotes | ACE2 | Gene:59272 |
| 335 | 706-710 | Gene | denotes | ACE2 | Gene:59272 |
| 336 | 935-939 | Gene | denotes | ACE2 | Gene:59272 |
| 337 | 99-104 | Gene | denotes | spike | Gene:43740568 |
| 338 | 43-47 | Species | denotes | nCOV | Tax:2697049 |
| 339 | 166-188 | Species | denotes | Bat coronavirus RaTG13 | Tax:2709072 |
| 340 | 225-229 | Species | denotes | nCOV | Tax:2697049 |
| 341 | 450-454 | Species | denotes | nCOV | Tax:2697049 |
| 342 | 589-593 | Species | denotes | nCOV | Tax:2697049 |
| 343 | 665-669 | Species | denotes | nCOV | Tax:2697049 |
| 344 | 1087-1091 | Species | denotes | nCOV | Tax:2697049 |
| 345 | 790-797 | Chemical | denotes | alanine | MESH:D000409 |
| 346 | 433-443 | CellLine | denotes | MN996532.1 | CVCL:U508 |
| 347 | 479-489 | CellLine | denotes | MN908947.1 | CVCL:U508 |